Re: [Rdkit-discuss] SMILES from sdf file

2021-09-13 Thread Anthony Nash
://www.kellogg.ox.ac.uk/ From: Patrick Walters Sent: 12 September 2021 15:27 To: Anthony Nash Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] SMILES from sdf file Hi Anthony, This is pretty easy and you don't need to use PandasTools (although PandasTools

Re: [Rdkit-discuss] SMILES from sdf file

2021-09-12 Thread Patrick Walters
Hi Anthony, This is pretty easy and you don't need to use PandasTools (although PandasTools are very cool). #!/usr/bin/env python import sys from rdkit import Chem suppl = Chem.SDMolSupplier(sys.argv[1]) for mol in suppl: if mol: print(Chem.MolToSmiles(mol),mol.GetProp("_Name"))

[Rdkit-discuss] SMILES from sdf file

2021-09-12 Thread Anthony Nash
Dear all, This sounded routine enough that I thought I'd seek guidance to save myself hours of hacking and potential misunderstanding. My objective is to generate a canonical SMILES for each compound in an sdf file. The sdf file was downloaded from ChEMBL and contains some +10,000 drugs. I've